importance {sjSDM}

importance

Description

Computes standardized variance components with respect to abiotic, biotic, and spatial effect groups.

Usage

importance(x, save_memory = TRUE, ...)

Arguments

x

object fitted by sjSDM or a list with beta, the association matrix, and the correlation matrix of the predictors, see details below

save_memory

use torch backend to calculate importance with single precision floats

...

additional arguments

Details

This variance partitioning approach is based on Ovaskainen et al., 2017. For an example how to interpret the outputs, see Leibold et al., 2021. This function will be deprecated in the future. Please use plot(anova(model), internal=TRUE) (currently only supported for spatial models).

Value

An S3 class of type 'sjSDMimportance' including the following components:

names

Character vector, species names.

res

Data frame of results.

spatial

Logical, spatial model or not.

Implemented S3 methods include print.sjSDMimportance and plot.sjSDMimportance

Author(s)

Maximilian Pichler

References

Ovaskainen, O., Tikhonov, G., Norberg, A., Guillaume Blanchet, F., Duan, L., Dunson, D., ... & Abrego, N. (2017). How to make more out of community data? A conceptual framework and its implementation as models and software. Ecology letters, 20(5), 561-576.

Leibold, M. A., Rudolph, F. J., Blanchet, F. G., De Meester, L., Gravel, D., Hartig, F., ... & Chase, J. M. (2021). The internal structure of metacommunities. Oikos.

See Also

print.sjSDMimportance, plot.sjSDMimportance

Examples

## Not run: 
library(sjSDM)
com = simulate_SDM(sites = 300L, species = 12L, 
                   link = "identical", response = "identical")
Raw = com$response
SP = matrix(rnorm(300*2), 300, 2)
SPweights = matrix(rnorm(12L), 1L)
SPweights[1,1:6] = 0
Y = Raw + (SP[,1,drop=FALSE]*SP[,2,drop=FALSE]) %*% SPweights
Y = ifelse(Y > 0, 1, 0)

model = sjSDM(Y = Y,env = linear(com$env_weights, lambda = 0.001), 
              spatial = linear(SP,formula = ~0+X1:X2, lambda = 0.001), 
              biotic = bioticStruct(lambda = 0.001),iter = 40L)
imp = importance(model)
plot(imp)

## End(Not run)